Starting phenix.real_space_refine
on Fri Aug 22 23:29:51 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8qju_18449/08_2025/8qju_18449.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qju_18449/08_2025/8qju_18449.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qju_18449/08_2025/8qju_18449.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qju_18449/08_2025/8qju_18449.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qju_18449/08_2025/8qju_18449.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qju_18449/08_2025/8qju_18449.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    5470      2.51       5
     N    1470      2.21       5
     O    1595      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 75 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8578
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1045, 8578
          Classifications: {'peptide': 1045}
          Link IDs: {'PTRANS': 46, 'TRANS': 998}
          Chain breaks: 4
  Time building chain proxies: 1.54, per 1000 atoms: 0.18
  Number of scatterers: 8578
  At special positions: 0
  Unit cell: (85.412, 104.32, 115.404, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      43     16.00
     O    1595      8.00
     N    1470      7.00
     C    5470      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 348 " - pdb=" SG  CYS A 353 " distance=2.07

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 243.7 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2004

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 15 sheets defined
      34.9% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 25
    Processing helix  chain 'A' and resid 79 through 83
      removed outlier: 3.768A  pdb=" N   PHE A  82 " --> pdb=" O   SER A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 136
      removed outlier: 3.919A  pdb=" N   ALA A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LYS A 127 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 154
      removed outlier: 3.558A  pdb=" N   GLU A 143 " --> pdb=" O   PRO A 139 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER A 144 " --> pdb=" O   THR A 140 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   ASP A 154 " --> pdb=" O   ILE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 173
      Proline residue:  A 171  - end of helix
    Processing helix  chain 'A' and resid 179 through 191
      removed outlier: 3.736A  pdb=" N   LEU A 183 " --> pdb=" O   SER A 179 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LYS A 184 " --> pdb=" O   ALA A 180 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLU A 189 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 222
      removed outlier: 3.580A  pdb=" N   PHE A 211 " --> pdb=" O   LYS A 207 " (cutoff:3.500A)
      removed outlier: 5.533A  pdb=" N   SER A 216 " --> pdb=" O   GLU A 212 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   ILE A 217 " --> pdb=" O   GLN A 213 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   LEU A 218 " --> pdb=" O   GLN A 214 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASP A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLU A 220 " --> pdb=" O   SER A 216 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   PHE A 221 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   LYS A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 252
    Processing helix  chain 'A' and resid 256 through 260
    Processing helix  chain 'A' and resid 261 through 274
    Processing helix  chain 'A' and resid 286 through 295
      removed outlier: 3.539A  pdb=" N   LEU A 291 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 300
    Processing helix  chain 'A' and resid 304 through 308
      removed outlier: 3.733A  pdb=" N   ALA A 308 " --> pdb=" O   LYS A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 315
      removed outlier: 3.623A  pdb=" N   ASN A 315 " --> pdb=" O   GLN A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 321
    Processing helix  chain 'A' and resid 341 through 352
      removed outlier: 3.976A  pdb=" N   TYR A 345 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 394
      removed outlier: 3.506A  pdb=" N   HIS A 392 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   PHE A 394 " --> pdb=" O   LYS A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 426
      removed outlier: 4.005A  pdb=" N   HIS A 416 " --> pdb=" O   GLU A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 429
      No H-bonds generated for 'chain 'A' and resid 427 through 429'
    Processing helix  chain 'A' and resid 526 through 530
    Processing helix  chain 'A' and resid 539 through 555
      removed outlier: 3.559A  pdb=" N   THR A 554 " --> pdb=" O   TYR A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 620
    Processing helix  chain 'A' and resid 639 through 644
      removed outlier: 3.835A  pdb=" N   SER A 643 " --> pdb=" O   ASN A 639 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   LYS A 644 " --> pdb=" O   PRO A 640 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 639 through 644'
    Processing helix  chain 'A' and resid 652 through 663
      removed outlier: 3.997A  pdb=" N   ILE A 663 " --> pdb=" O   MET A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 723
    Processing helix  chain 'A' and resid 736 through 743
      removed outlier: 3.753A  pdb=" N   ARG A 742 " --> pdb=" O   GLU A 738 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 843
      removed outlier: 3.624A  pdb=" N   ASP A 842 " --> pdb=" O   GLN A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 849
    Processing helix  chain 'A' and resid 892 through 908
    Processing helix  chain 'A' and resid 927 through 934
      removed outlier: 3.604A  pdb=" N   VAL A 934 " --> pdb=" O   LEU A 930 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 970
    Processing helix  chain 'A' and resid 970 through 979
      removed outlier: 4.660A  pdb=" N   LEU A 974 " --> pdb=" O   LYS A 970 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LEU A 975 " --> pdb=" O   PRO A 971 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 999 through 1005
    Processing helix  chain 'A' and resid 1018 through 1030
    Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 66
      removed outlier: 3.968A  pdb=" N   GLY A  63 " --> pdb=" O   TRP A  54 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLU A  39 " --> pdb=" O   VAL A  30 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   ARG A  41 " --> pdb=" O   MET A  28 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   MET A  28 " --> pdb=" O   ARG A  41 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   SER A 110 " --> pdb=" O   PHE A  31 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   SER A 107 " --> pdb=" O   TYR A 100 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLU A  72 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 162
    Processing sheet with id=AA3, first strand: chain 'A' and resid 241 through 242
    Processing sheet with id=AA4, first strand: chain 'A' and resid 331 through 332
      removed outlier: 3.665A  pdb=" N   THR A 332 " --> pdb=" O   GLU A 339 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLU A 339 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 369 through 370
    Processing sheet with id=AA6, first strand: chain 'A' and resid 851 through 854
    Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 565
    Processing sheet with id=AA8, first strand: chain 'A' and resid 622 through 624
    Processing sheet with id=AA9, first strand: chain 'A' and resid 647 through 648
      removed outlier: 3.866A  pdb=" N   ALA A 668 " --> pdb=" O   ARG A 685 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   TYR A 680 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE A 682 " --> pdb=" O   CYS A 693 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   PHE A 684 " --> pdb=" O   LYS A 691 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS A 691 " --> pdb=" O   PHE A 684 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ASN A 696 " --> pdb=" O   VAL A 703 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 647 through 648
    Processing sheet with id=AB2, first strand: chain 'A' and resid 858 through 862
      removed outlier: 3.662A  pdb=" N   GLU A 877 " --> pdb=" O   ASN A 859 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 938 through 939
      removed outlier: 5.077A  pdb=" N   LYS A 938 " --> pdb=" O   ILE A 955 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   GLU A 954 " --> pdb=" O   LEU A 982 " (cutoff:3.500A)
      removed outlier: 8.333A  pdb=" N   ARG A 984 " --> pdb=" O   GLU A 954 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   ARG A 956 " --> pdb=" O   ARG A 984 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   THR A 983 " --> pdb=" O   MET A1009 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1061 through 1063
      removed outlier: 4.292A  pdb=" N   ARG A1187 " --> pdb=" O   THR A1062 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1098 through 1100
      removed outlier: 3.997A  pdb=" N   VAL A1087 " --> pdb=" O   PHE A1099 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   CYS A1082 " --> pdb=" O   GLU A1139 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   GLU A1138 " --> pdb=" O   PHE A1147 " (cutoff:3.500A)
      removed outlier: 5.337A  pdb=" N   PHE A1147 " --> pdb=" O   GLU A1138 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ASP A1140 " --> pdb=" O   PRO A1145 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1163 through 1164

    300 hydrogen bonds defined for protein.
    816 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.29

  Time building geometry restraints manager: 0.80 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.18 -     1.31: 1421
        1.31 -     1.44: 2389
        1.44 -     1.57: 4901
        1.57 -     1.70: 0
        1.70 -     1.83: 68
  Bond restraints: 8779
  Sorted by residual:
  bond pdb=" C   THR A1102 "
       pdb=" O   THR A1102 "
    ideal  model  delta    sigma   weight residual
    1.234  1.182  0.051 1.17e-02 7.31e+03 1.92e+01
  bond pdb=" CA  SER A1110 "
       pdb=" CB  SER A1110 "
    ideal  model  delta    sigma   weight residual
    1.528  1.487  0.040 1.14e-02 7.69e+03 1.25e+01
  bond pdb=" CA  SER A 110 "
       pdb=" CB  SER A 110 "
    ideal  model  delta    sigma   weight residual
    1.530  1.483  0.047 1.50e-02 4.44e+03 1.00e+01
  bond pdb=" N   LEU A1073 "
       pdb=" CA  LEU A1073 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.14e-02 7.69e+03 8.07e+00
  bond pdb=" CA  SER A1172 "
       pdb=" CB  SER A1172 "
    ideal  model  delta    sigma   weight residual
    1.523  1.491  0.033 1.21e-02 6.83e+03 7.25e+00
  ... (remaining 8774 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 10759
        2.42 -     4.83: 990
        4.83 -     7.25: 82
        7.25 -     9.66: 15
        9.66 -    12.08: 3
  Bond angle restraints: 11849
  Sorted by residual:
  angle pdb=" N   PRO A 400 "
        pdb=" CA  PRO A 400 "
        pdb=" C   PRO A 400 "
      ideal   model   delta    sigma   weight residual
     111.32  123.40  -12.08 1.71e+00 3.42e-01 4.99e+01
  angle pdb=" N   PRO A  75 "
        pdb=" CA  PRO A  75 "
        pdb=" C   PRO A  75 "
      ideal   model   delta    sigma   weight residual
     113.57  122.36   -8.79 1.31e+00 5.83e-01 4.50e+01
  angle pdb=" C   PRO A 400 "
        pdb=" CA  PRO A 400 "
        pdb=" CB  PRO A 400 "
      ideal   model   delta    sigma   weight residual
     110.85  101.65    9.20 1.41e+00 5.03e-01 4.25e+01
  angle pdb=" C   PRO A  75 "
        pdb=" CA  PRO A  75 "
        pdb=" CB  PRO A  75 "
      ideal   model   delta    sigma   weight residual
     112.11  103.18    8.93 1.46e+00 4.69e-01 3.74e+01
  angle pdb=" CA  PHE A 505 "
        pdb=" CB  PHE A 505 "
        pdb=" CG  PHE A 505 "
      ideal   model   delta    sigma   weight residual
     113.80  119.26   -5.46 1.00e+00 1.00e+00 2.98e+01
  ... (remaining 11844 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.12: 4702
       17.12 -    34.23: 442
       34.23 -    51.34: 96
       51.34 -    68.46: 88
       68.46 -    85.57: 2
  Dihedral angle restraints: 5330
    sinusoidal: 2245
      harmonic: 3085
  Sorted by residual:
  dihedral pdb=" CB  CYS A 348 "
           pdb=" SG  CYS A 348 "
           pdb=" SG  CYS A 353 "
           pdb=" CB  CYS A 353 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.46  -60.46     1      1.00e+01 1.00e-02 4.87e+01
  dihedral pdb=" CA  ALA A 259 "
           pdb=" C   ALA A 259 "
           pdb=" N   GLN A 260 "
           pdb=" CA  GLN A 260 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.62   27.38     0      5.00e+00 4.00e-02 3.00e+01
  dihedral pdb=" CA  THR A 706 "
           pdb=" C   THR A 706 "
           pdb=" N   SER A 707 "
           pdb=" CA  SER A 707 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.07  -25.93     0      5.00e+00 4.00e-02 2.69e+01
  ... (remaining 5327 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 902
       0.083 -    0.166: 332
       0.166 -    0.249: 34
       0.249 -    0.332: 4
       0.332 -    0.415: 1
  Chirality restraints: 1273
  Sorted by residual:
  chirality pdb=" CA  PHE A1028 "
            pdb=" N   PHE A1028 "
            pdb=" C   PHE A1028 "
            pdb=" CB  PHE A1028 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.30e+00
  chirality pdb=" CA  TYR A1020 "
            pdb=" N   TYR A1020 "
            pdb=" C   TYR A1020 "
            pdb=" CB  TYR A1020 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.23e+00
  chirality pdb=" CA  ARG A 248 "
            pdb=" N   ARG A 248 "
            pdb=" C   ARG A 248 "
            pdb=" CB  ARG A 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.05e+00
  ... (remaining 1270 not shown)

  Planarity restraints: 1521
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 679 "   -0.015 2.00e-02 2.50e+03   3.10e-02 9.63e+00
        pdb=" C   SER A 679 "    0.054 2.00e-02 2.50e+03
        pdb=" O   SER A 679 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   TYR A 680 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 147 "   -0.260 9.50e-02 1.11e+02   1.17e-01 8.71e+00
        pdb=" NE  ARG A 147 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 147 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 147 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 147 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A1153 "    0.039 2.00e-02 2.50e+03   2.01e-02 8.05e+00
        pdb=" CG  TYR A1153 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR A1153 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD2 TYR A1153 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE1 TYR A1153 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR A1153 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A1153 "    0.008 2.00e-02 2.50e+03
        pdb=" OH  TYR A1153 "    0.022 2.00e-02 2.50e+03
  ... (remaining 1518 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1683
        2.77 -     3.31: 8974
        3.31 -     3.84: 13878
        3.84 -     4.37: 16841
        4.37 -     4.90: 27064
  Nonbonded interactions: 68440
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 647 "
            pdb=" NZ  LYS A 673 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" O   PRO A 400 "
            pdb=" OH  TYR A1036 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   THR A 332 "
            pdb=" OG  SER A 338 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   ARG A 700 "
            pdb=" ND1 HIS A 701 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" O   GLU A 279 "
            pdb=" OG1 THR A 280 "
     model   vdw
     2.285 3.040
  ... (remaining 68435 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.950
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051   8780  Z= 0.500
  Angle     :  1.446  12.078  11851  Z= 0.979
  Chirality :  0.078   0.415   1273
  Planarity :  0.010   0.117   1521
  Dihedral  : 16.446  85.571   3323
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 31.96
  Ramachandran Plot:
    Outliers :  2.13 %
    Allowed  :  8.79 %
    Favored  : 89.08 %
  Rotamer:
    Outliers : 10.42 %
    Allowed  : 12.21 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.58 (0.23), residues: 1035
  helix: -1.69 (0.25), residues: 284
  sheet: -1.34 (0.37), residues: 198
  loop : -1.84 (0.23), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.002   ARG A 158 
 TYR   0.039   0.006   TYR A1153 
 PHE   0.036   0.004   PHE A 505 
 TRP   0.030   0.005   TRP A 322 
 HIS   0.008   0.002   HIS A 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00732 ( 8779)
  covalent geometry    : angle       1.44624 (11849)
  SS BOND              : bond        0.03762 (    1)
  SS BOND              : angle       2.00407 (    2)
  hydrogen bonds       : bond        0.26608 (  298)
  hydrogen bonds       : angle       9.82690 (  816)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  401 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 99
    poor density    : 302
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.8445 (tp40) cc_final: 0.7998 (tm-30)
REVERT: A   20 ARG cc_start: 0.8323 (tpp-160) cc_final: 0.7911 (tmm-80)
REVERT: A   28 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8138 (mtp)
REVERT: A   68 MET cc_start: 0.8701 (mmm) cc_final: 0.8441 (mtt)
REVERT: A   93 ASP cc_start: 0.8354 (t0) cc_final: 0.7788 (p0)
REVERT: A  164 ARG cc_start: 0.9134 (ttt-90) cc_final: 0.8926 (ttm110)
REVERT: A  186 LYS cc_start: 0.6226 (OUTLIER) cc_final: 0.5787 (mmtp)
REVERT: A  196 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8412 (tp30)
REVERT: A  200 GLU cc_start: 0.9032 (mp0) cc_final: 0.8692 (tp30)
REVERT: A  249 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.8298 (t80)
REVERT: A  289 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8184 (mp0)
REVERT: A  314 MET cc_start: 0.8018 (mmm) cc_final: 0.7160 (mmm)
REVERT: A  320 HIS cc_start: 0.8230 (m90) cc_final: 0.7656 (m-70)
REVERT: A  409 CYS cc_start: 0.8826 (m) cc_final: 0.8431 (m)
REVERT: A  484 TRP cc_start: 0.7483 (t-100) cc_final: 0.7224 (t-100)
REVERT: A  592 MET cc_start: -0.3752 (mtt) cc_final: -0.3980 (pmm)
REVERT: A  646 TRP cc_start: 0.8388 (p-90) cc_final: 0.7671 (p-90)
REVERT: A  651 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8762 (tp)
REVERT: A  652 SER cc_start: 0.8620 (t) cc_final: 0.8225 (p)
REVERT: A  693 CYS cc_start: 0.8484 (t) cc_final: 0.8098 (p)
REVERT: A  728 LYS cc_start: 0.9237 (mptm) cc_final: 0.8858 (tmtt)
REVERT: A  729 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.9018 (ppp)
REVERT: A  859 ASN cc_start: 0.8504 (m-40) cc_final: 0.8278 (p0)
REVERT: A  868 ASN cc_start: 0.8457 (m-40) cc_final: 0.8115 (m-40)
REVERT: A  873 VAL cc_start: 0.9324 (p) cc_final: 0.9105 (t)
REVERT: A  886 VAL cc_start: 0.8619 (t) cc_final: 0.8395 (m)
REVERT: A  938 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7869 (ttmm)
REVERT: A  953 ARG cc_start: 0.8846 (ptp-110) cc_final: 0.8502 (mtm-85)
REVERT: A  970 LYS cc_start: 0.5774 (OUTLIER) cc_final: 0.4598 (pptt)
REVERT: A  997 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7773 (p90)
REVERT: A 1039 GLN cc_start: 0.8916 (mt0) cc_final: 0.8674 (mt0)
REVERT: A 1051 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8998 (mmm)
REVERT: A 1110 SER cc_start: 0.9044 (p) cc_final: 0.8843 (t)
REVERT: A 1141 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8746 (mtm)
REVERT: A 1164 SER cc_start: 0.8829 (t) cc_final: 0.8407 (p)
REVERT: A 1176 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8208 (mm-30)
REVERT: A 1186 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.9009 (mtm)
  outliers start: 99
  outliers final: 42
  residues processed: 361
  average time/residue: 0.0755
  time to fit residues: 36.6156
Evaluate side-chains
  279 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 225
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   89 ARG
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  118 ASP
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  157 ARG
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  186 LYS
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  242 TYR
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  249 PHE
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  477 GLN
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  496 CYS
Chi-restraints excluded: chain A residue  636 PRO
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  680 TYR
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  692 HIS
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  970 LYS
Chi-restraints excluded: chain A residue  997 TYR
Chi-restraints excluded: chain A residue 1014 PHE
Chi-restraints excluded: chain A residue 1021 MET
Chi-restraints excluded: chain A residue 1025 HIS
Chi-restraints excluded: chain A residue 1051 MET
Chi-restraints excluded: chain A residue 1096 ASN
Chi-restraints excluded: chain A residue 1102 THR
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain A residue 1120 VAL
Chi-restraints excluded: chain A residue 1138 GLU
Chi-restraints excluded: chain A residue 1141 MET
Chi-restraints excluded: chain A residue 1142 PHE
Chi-restraints excluded: chain A residue 1155 ILE
Chi-restraints excluded: chain A residue 1158 VAL
Chi-restraints excluded: chain A residue 1186 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  51 GLN
A 121 ASN
A 201 GLN
A 247 GLN
A 260 GLN
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 372 HIS
A 387 GLN
A 413 GLN
A 446 GLN
A 616 HIS
A 637 ASN
A 856 ASN
A 868 ASN
A 979 GLN
** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1031 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.132902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.099722 restraints weight = 14242.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.103751 restraints weight = 6557.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.106411 restraints weight = 3945.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.108100 restraints weight = 2805.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.109291 restraints weight = 2239.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.3274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8780  Z= 0.177
  Angle     :  0.749   9.282  11851  Z= 0.403
  Chirality :  0.046   0.216   1273
  Planarity :  0.006   0.105   1521
  Dihedral  : 10.896  61.815   1262
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  6.38 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  6.53 %
    Allowed  : 17.47 %
    Favored  : 76.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.23 (0.25), residues: 1035
  helix:  0.58 (0.28), residues: 311
  sheet: -0.98 (0.35), residues: 211
  loop : -1.64 (0.25), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  74 
 TYR   0.019   0.002   TYR A1137 
 PHE   0.021   0.002   PHE A 272 
 TRP   0.020   0.002   TRP A  54 
 HIS   0.005   0.001   HIS A 534 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 8779)
  covalent geometry    : angle       0.74879 (11849)
  SS BOND              : bond        0.00190 (    1)
  SS BOND              : angle       1.37548 (    2)
  hydrogen bonds       : bond        0.05046 (  298)
  hydrogen bonds       : angle       5.77901 (  816)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 228
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.7805 (tp40) cc_final: 0.7348 (tm-30)
REVERT: A   20 ARG cc_start: 0.7985 (tpp-160) cc_final: 0.7332 (tmm-80)
REVERT: A   28 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7652 (ptp)
REVERT: A   89 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8203 (tpm170)
REVERT: A  214 GLN cc_start: 0.8277 (mt0) cc_final: 0.7811 (mt0)
REVERT: A  314 MET cc_start: 0.7766 (mmm) cc_final: 0.6686 (mmt)
REVERT: A  320 HIS cc_start: 0.7887 (m90) cc_final: 0.7092 (m-70)
REVERT: A  355 CYS cc_start: 0.7304 (t) cc_final: 0.6962 (t)
REVERT: A  361 TRP cc_start: 0.8175 (m100) cc_final: 0.7878 (m100)
REVERT: A  449 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7400 (tt0)
REVERT: A  477 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7564 (tp-100)
REVERT: A  548 GLN cc_start: 0.8814 (pt0) cc_final: 0.8485 (pm20)
REVERT: A  646 TRP cc_start: 0.7905 (p-90) cc_final: 0.7168 (p-90)
REVERT: A  651 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8407 (tp)
REVERT: A  658 ASP cc_start: 0.8903 (m-30) cc_final: 0.8512 (m-30)
REVERT: A  693 CYS cc_start: 0.7256 (t) cc_final: 0.7039 (p)
REVERT: A  859 ASN cc_start: 0.7646 (m-40) cc_final: 0.7436 (p0)
REVERT: A  873 VAL cc_start: 0.9319 (p) cc_final: 0.9041 (t)
REVERT: A  895 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7261 (mp0)
REVERT: A  897 PHE cc_start: 0.8574 (t80) cc_final: 0.8241 (t80)
REVERT: A  898 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8374 (mt-10)
REVERT: A  946 ASN cc_start: 0.7860 (t0) cc_final: 0.7505 (t0)
REVERT: A  960 GLU cc_start: 0.7475 (pt0) cc_final: 0.7101 (pt0)
REVERT: A  964 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7908 (t0)
REVERT: A  978 ASN cc_start: 0.8062 (m-40) cc_final: 0.7382 (t0)
REVERT: A 1009 MET cc_start: 0.7494 (mtt) cc_final: 0.6973 (mtt)
REVERT: A 1039 GLN cc_start: 0.8467 (mt0) cc_final: 0.8080 (mt0)
REVERT: A 1045 THR cc_start: 0.7618 (p) cc_final: 0.7316 (p)
REVERT: A 1061 MET cc_start: 0.7156 (mtt) cc_final: 0.6685 (ttt)
REVERT: A 1105 ASN cc_start: 0.8203 (t0) cc_final: 0.7973 (m-40)
REVERT: A 1110 SER cc_start: 0.8585 (p) cc_final: 0.8239 (t)
REVERT: A 1152 THR cc_start: 0.8682 (m) cc_final: 0.8316 (p)
  outliers start: 62
  outliers final: 28
  residues processed: 271
  average time/residue: 0.0636
  time to fit residues: 24.1983
Evaluate side-chains
  229 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 195
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   89 ARG
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  157 ARG
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  237 ASP
Chi-restraints excluded: chain A residue  242 TYR
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  477 GLN
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  692 HIS
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  895 GLU
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  964 ASP
Chi-restraints excluded: chain A residue 1096 ASN
Chi-restraints excluded: chain A residue 1102 THR
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain A residue 1138 GLU
Chi-restraints excluded: chain A residue 1142 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 63 optimal weight:    7.9990
   chunk 75 optimal weight:    6.9990
   chunk 66 optimal weight:    0.0770
   chunk 58 optimal weight:   20.0000
   chunk 69 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0470
   chunk 97 optimal weight:    0.0370
   chunk 0 optimal weight:    8.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    0.4114

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 455 HIS
A 868 ASN
** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.135280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.102391 restraints weight = 14084.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.106513 restraints weight = 6463.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.109237 restraints weight = 3853.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.111012 restraints weight = 2707.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.111923 restraints weight = 2135.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
moved from start:          0.4222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8780  Z= 0.130
  Angle     :  0.648   7.018  11851  Z= 0.344
  Chirality :  0.043   0.292   1273
  Planarity :  0.005   0.042   1521
  Dihedral  :  8.545  59.556   1193
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  6.76 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 20.74 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.17 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.64 (0.26), residues: 1035
  helix:  1.52 (0.29), residues: 311
  sheet: -0.82 (0.35), residues: 218
  loop : -1.51 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1057 
 TYR   0.018   0.001   TYR A1094 
 PHE   0.022   0.002   PHE A 272 
 TRP   0.018   0.001   TRP A  54 
 HIS   0.004   0.001   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8779)
  covalent geometry    : angle       0.64821 (11849)
  SS BOND              : bond        0.00295 (    1)
  SS BOND              : angle       1.20373 (    2)
  hydrogen bonds       : bond        0.03976 (  298)
  hydrogen bonds       : angle       5.06009 (  816)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 221
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.7678 (tp40) cc_final: 0.7330 (tm-30)
REVERT: A   20 ARG cc_start: 0.7932 (tpp-160) cc_final: 0.7226 (tmm-80)
REVERT: A   28 MET cc_start: 0.7954 (ptp) cc_final: 0.7752 (ptp)
REVERT: A   92 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6519 (tt0)
REVERT: A   93 ASP cc_start: 0.7564 (t0) cc_final: 0.7332 (t0)
REVERT: A  210 MET cc_start: 0.8168 (mmm) cc_final: 0.7013 (mmm)
REVERT: A  235 ARG cc_start: 0.8187 (ttp-110) cc_final: 0.7840 (ptp90)
REVERT: A  320 HIS cc_start: 0.7805 (m90) cc_final: 0.7453 (m90)
REVERT: A  354 ARG cc_start: 0.5901 (OUTLIER) cc_final: 0.5674 (mmt180)
REVERT: A  359 ASP cc_start: 0.6046 (m-30) cc_final: 0.5437 (m-30)
REVERT: A  379 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7300 (mmtt)
REVERT: A  417 MET cc_start: 0.8068 (ttm) cc_final: 0.7582 (ttm)
REVERT: A  477 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7684 (tp-100)
REVERT: A  548 GLN cc_start: 0.8934 (pt0) cc_final: 0.8506 (pm20)
REVERT: A  658 ASP cc_start: 0.8907 (m-30) cc_final: 0.8440 (m-30)
REVERT: A  659 MET cc_start: 0.8012 (tpp) cc_final: 0.7776 (tpp)
REVERT: A  700 ARG cc_start: 0.9004 (ttp80) cc_final: 0.8495 (ttp80)
REVERT: A  895 GLU cc_start: 0.8019 (mp0) cc_final: 0.7330 (mp0)
REVERT: A  897 PHE cc_start: 0.8637 (t80) cc_final: 0.8337 (t80)
REVERT: A  901 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8387 (mm110)
REVERT: A  929 GLU cc_start: 0.8043 (pm20) cc_final: 0.7738 (mp0)
REVERT: A  946 ASN cc_start: 0.7866 (t0) cc_final: 0.7472 (t0)
REVERT: A  960 GLU cc_start: 0.7498 (pt0) cc_final: 0.7044 (pt0)
REVERT: A  964 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7921 (t0)
REVERT: A  978 ASN cc_start: 0.8095 (m-40) cc_final: 0.7452 (t0)
REVERT: A  996 ASN cc_start: 0.8253 (m-40) cc_final: 0.7986 (m-40)
REVERT: A 1004 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8856 (tt)
REVERT: A 1009 MET cc_start: 0.7032 (mtt) cc_final: 0.6682 (mtt)
REVERT: A 1045 THR cc_start: 0.7657 (p) cc_final: 0.7449 (p)
REVERT: A 1048 TYR cc_start: 0.7995 (t80) cc_final: 0.7789 (t80)
REVERT: A 1051 MET cc_start: 0.8897 (mmm) cc_final: 0.8684 (mmm)
REVERT: A 1105 ASN cc_start: 0.8178 (t0) cc_final: 0.7960 (m-40)
REVERT: A 1135 VAL cc_start: 0.8812 (m) cc_final: 0.8431 (p)
REVERT: A 1158 VAL cc_start: 0.8333 (t) cc_final: 0.7982 (p)
  outliers start: 42
  outliers final: 24
  residues processed: 246
  average time/residue: 0.0664
  time to fit residues: 22.8081
Evaluate side-chains
  210 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 180
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  477 GLN
Chi-restraints excluded: chain A residue  485 ASP
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  692 HIS
Chi-restraints excluded: chain A residue  722 LYS
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  868 ASN
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  964 ASP
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1096 ASN
Chi-restraints excluded: chain A residue 1102 THR
Chi-restraints excluded: chain A residue 1142 PHE
Chi-restraints excluded: chain A residue 1152 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 60 optimal weight:    8.9990
   chunk 33 optimal weight:    0.8980
   chunk 89 optimal weight:    0.1980
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 98 optimal weight:    0.5980
   chunk 78 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 868 ASN
** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.140305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.106947 restraints weight = 14017.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.111231 restraints weight = 6204.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.114014 restraints weight = 3642.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.115830 restraints weight = 2550.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.116675 restraints weight = 2016.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.4626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8780  Z= 0.136
  Angle     :  0.625   9.355  11851  Z= 0.328
  Chirality :  0.042   0.225   1273
  Planarity :  0.005   0.068   1521
  Dihedral  :  7.593  58.397   1172
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  7.25 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 21.47 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.17 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.26), residues: 1035
  helix:  1.67 (0.30), residues: 305
  sheet: -0.53 (0.36), residues: 212
  loop : -1.45 (0.26), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1057 
 TYR   0.019   0.001   TYR A1094 
 PHE   0.033   0.002   PHE A 272 
 TRP   0.012   0.001   TRP A 258 
 HIS   0.004   0.001   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8779)
  covalent geometry    : angle       0.62501 (11849)
  SS BOND              : bond        0.00263 (    1)
  SS BOND              : angle       0.98267 (    2)
  hydrogen bonds       : bond        0.03718 (  298)
  hydrogen bonds       : angle       4.82784 (  816)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 194
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.7631 (tp40) cc_final: 0.7374 (tm-30)
REVERT: A   20 ARG cc_start: 0.7987 (tpp-160) cc_final: 0.7284 (tmm-80)
REVERT: A  206 TYR cc_start: 0.7494 (t80) cc_final: 0.7260 (t80)
REVERT: A  210 MET cc_start: 0.8135 (mmm) cc_final: 0.7037 (mmm)
REVERT: A  235 ARG cc_start: 0.8119 (ttp-110) cc_final: 0.7814 (ptp90)
REVERT: A  320 HIS cc_start: 0.7830 (m90) cc_final: 0.7340 (m-70)
REVERT: A  354 ARG cc_start: 0.6125 (OUTLIER) cc_final: 0.5890 (mmt180)
REVERT: A  359 ASP cc_start: 0.6156 (m-30) cc_final: 0.5764 (m-30)
REVERT: A  417 MET cc_start: 0.8023 (ttm) cc_final: 0.7766 (ttm)
REVERT: A  477 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7682 (tp-100)
REVERT: A  548 GLN cc_start: 0.9002 (pt0) cc_final: 0.8510 (pm20)
REVERT: A  658 ASP cc_start: 0.8897 (m-30) cc_final: 0.8448 (m-30)
REVERT: A  700 ARG cc_start: 0.9135 (ttp80) cc_final: 0.8651 (ttp80)
REVERT: A  900 PHE cc_start: 0.8869 (t80) cc_final: 0.8402 (t80)
REVERT: A  946 ASN cc_start: 0.7697 (t0) cc_final: 0.7197 (t0)
REVERT: A  964 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7828 (t0)
REVERT: A  978 ASN cc_start: 0.8091 (m-40) cc_final: 0.7507 (t0)
REVERT: A  996 ASN cc_start: 0.8305 (m-40) cc_final: 0.8025 (m-40)
REVERT: A 1004 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8821 (tt)
REVERT: A 1009 MET cc_start: 0.7058 (mtt) cc_final: 0.6809 (mtt)
REVERT: A 1152 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8315 (p)
REVERT: A 1186 MET cc_start: 0.7805 (mtm) cc_final: 0.7447 (mtm)
  outliers start: 47
  outliers final: 29
  residues processed: 224
  average time/residue: 0.0676
  time to fit residues: 21.4842
Evaluate side-chains
  212 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 178
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  365 ASP
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  477 GLN
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  692 HIS
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  722 LYS
Chi-restraints excluded: chain A residue  728 LYS
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  868 ASN
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  964 ASP
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1096 ASN
Chi-restraints excluded: chain A residue 1102 THR
Chi-restraints excluded: chain A residue 1142 PHE
Chi-restraints excluded: chain A residue 1152 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 91 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0670
   chunk 22 optimal weight:    0.1980
   chunk 92 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 72 optimal weight:    3.9990
   chunk 98 optimal weight:    0.8980
   chunk 2 optimal weight:    6.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    0.5118

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.141639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.108452 restraints weight = 14008.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.112758 restraints weight = 6160.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.115490 restraints weight = 3630.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.117271 restraints weight = 2574.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.118683 restraints weight = 2049.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.4995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8780  Z= 0.125
  Angle     :  0.618  10.102  11851  Z= 0.323
  Chirality :  0.042   0.305   1273
  Planarity :  0.004   0.049   1521
  Dihedral  :  7.144  58.721   1169
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  7.34 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 22.21 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.17 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.34 (0.27), residues: 1035
  helix:  1.73 (0.30), residues: 305
  sheet: -0.53 (0.35), residues: 227
  loop : -1.34 (0.27), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1057 
 TYR   0.014   0.001   TYR A1048 
 PHE   0.038   0.002   PHE A 272 
 TRP   0.038   0.002   TRP A 145 
 HIS   0.004   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8779)
  covalent geometry    : angle       0.61799 (11849)
  SS BOND              : bond        0.00201 (    1)
  SS BOND              : angle       0.90349 (    2)
  hydrogen bonds       : bond        0.03511 (  298)
  hydrogen bonds       : angle       4.69683 (  816)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 194
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.7626 (tp40) cc_final: 0.7271 (tm-30)
REVERT: A   20 ARG cc_start: 0.7904 (tpp-160) cc_final: 0.7181 (tmm-80)
REVERT: A   69 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7323 (mm-30)
REVERT: A  190 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.8023 (mp)
REVERT: A  210 MET cc_start: 0.7993 (mmm) cc_final: 0.7442 (mmm)
REVERT: A  235 ARG cc_start: 0.8092 (ttp-110) cc_final: 0.7777 (ptp90)
REVERT: A  320 HIS cc_start: 0.7879 (m90) cc_final: 0.7307 (m-70)
REVERT: A  359 ASP cc_start: 0.6060 (m-30) cc_final: 0.5683 (m-30)
REVERT: A  379 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7474 (mmtt)
REVERT: A  417 MET cc_start: 0.7991 (ttm) cc_final: 0.7774 (ttm)
REVERT: A  477 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7677 (tp-100)
REVERT: A  548 GLN cc_start: 0.9036 (pt0) cc_final: 0.8518 (pm20)
REVERT: A  658 ASP cc_start: 0.8964 (m-30) cc_final: 0.8470 (m-30)
REVERT: A  700 ARG cc_start: 0.9153 (ttp80) cc_final: 0.8711 (ttp80)
REVERT: A  868 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.6696 (t0)
REVERT: A  946 ASN cc_start: 0.7772 (t0) cc_final: 0.7258 (t0)
REVERT: A  964 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7884 (t0)
REVERT: A  978 ASN cc_start: 0.8105 (m-40) cc_final: 0.7540 (t0)
REVERT: A 1004 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9020 (tt)
REVERT: A 1009 MET cc_start: 0.7118 (mtt) cc_final: 0.6891 (mtt)
REVERT: A 1045 THR cc_start: 0.7799 (p) cc_final: 0.7516 (p)
REVERT: A 1110 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.7807 (t)
REVERT: A 1152 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8305 (p)
REVERT: A 1186 MET cc_start: 0.7896 (mtm) cc_final: 0.7558 (mtm)
  outliers start: 44
  outliers final: 26
  residues processed: 218
  average time/residue: 0.0624
  time to fit residues: 19.1250
Evaluate side-chains
  214 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 180
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  477 GLN
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  496 CYS
Chi-restraints excluded: chain A residue  692 HIS
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  722 LYS
Chi-restraints excluded: chain A residue  728 LYS
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  868 ASN
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  964 ASP
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1096 ASN
Chi-restraints excluded: chain A residue 1110 SER
Chi-restraints excluded: chain A residue 1124 ILE
Chi-restraints excluded: chain A residue 1142 PHE
Chi-restraints excluded: chain A residue 1152 THR
Chi-restraints excluded: chain A residue 1182 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 56 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9990
   chunk 53 optimal weight:    9.9990
   chunk 17 optimal weight:    0.5980
   chunk 43 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0070
   chunk 13 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0870
   chunk 55 optimal weight:    6.9990
   overall best weight:    0.4176

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 201 GLN
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 475 HIS
A 868 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.142791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.110111 restraints weight = 13768.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.114432 restraints weight = 6042.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.117142 restraints weight = 3533.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.118771 restraints weight = 2498.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.119953 restraints weight = 1996.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.5313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8780  Z= 0.118
  Angle     :  0.615   9.652  11851  Z= 0.319
  Chirality :  0.041   0.260   1273
  Planarity :  0.004   0.048   1521
  Dihedral  :  6.647  56.847   1165
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  7.25 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 22.74 %
    Favored  : 72.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.42 (0.27), residues: 1035
  helix:  1.65 (0.30), residues: 312
  sheet: -0.58 (0.35), residues: 226
  loop : -1.42 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 742 
 TYR   0.019   0.001   TYR A 371 
 PHE   0.026   0.002   PHE A 272 
 TRP   0.023   0.001   TRP A 145 
 HIS   0.004   0.001   HIS A 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8779)
  covalent geometry    : angle       0.61516 (11849)
  SS BOND              : bond        0.00081 (    1)
  SS BOND              : angle       1.21812 (    2)
  hydrogen bonds       : bond        0.03419 (  298)
  hydrogen bonds       : angle       4.58080 (  816)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 193
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.7562 (tp40) cc_final: 0.7235 (tm-30)
REVERT: A   20 ARG cc_start: 0.7897 (tpp-160) cc_final: 0.7181 (tmm-80)
REVERT: A   69 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7341 (mm-30)
REVERT: A  135 ASN cc_start: 0.8471 (t0) cc_final: 0.7521 (p0)
REVERT: A  210 MET cc_start: 0.7973 (mmm) cc_final: 0.7443 (mmm)
REVERT: A  235 ARG cc_start: 0.8062 (ttp-110) cc_final: 0.7704 (ptp90)
REVERT: A  272 PHE cc_start: 0.8087 (t80) cc_final: 0.7869 (t80)
REVERT: A  359 ASP cc_start: 0.6056 (m-30) cc_final: 0.5657 (m-30)
REVERT: A  379 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7599 (mmtt)
REVERT: A  548 GLN cc_start: 0.9055 (pt0) cc_final: 0.8534 (pm20)
REVERT: A  658 ASP cc_start: 0.8924 (m-30) cc_final: 0.8430 (m-30)
REVERT: A  700 ARG cc_start: 0.9162 (ttp80) cc_final: 0.8351 (ttp80)
REVERT: A  701 HIS cc_start: 0.7787 (OUTLIER) cc_final: 0.7457 (m-70)
REVERT: A  897 PHE cc_start: 0.8700 (t80) cc_final: 0.8396 (t80)
REVERT: A  946 ASN cc_start: 0.7693 (t0) cc_final: 0.7191 (t0)
REVERT: A  978 ASN cc_start: 0.8056 (m-40) cc_final: 0.7513 (t0)
REVERT: A 1061 MET cc_start: 0.6403 (ttt) cc_final: 0.6188 (ttt)
REVERT: A 1152 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8312 (p)
  outliers start: 42
  outliers final: 25
  residues processed: 217
  average time/residue: 0.0637
  time to fit residues: 19.6458
Evaluate side-chains
  208 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 180
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  693 CYS
Chi-restraints excluded: chain A residue  701 HIS
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  722 LYS
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1060 LEU
Chi-restraints excluded: chain A residue 1135 VAL
Chi-restraints excluded: chain A residue 1142 PHE
Chi-restraints excluded: chain A residue 1152 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 50 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 79 optimal weight:    0.3980
   chunk 92 optimal weight:    0.0370
   chunk 45 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.5458

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 475 HIS
A 478 GLN
A1025 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.141703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.108296 restraints weight = 13816.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.112611 restraints weight = 6075.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.115387 restraints weight = 3564.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.117265 restraints weight = 2524.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.118319 restraints weight = 1998.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.5450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8780  Z= 0.124
  Angle     :  0.625   9.495  11851  Z= 0.323
  Chirality :  0.041   0.232   1273
  Planarity :  0.004   0.050   1521
  Dihedral  :  5.905  57.358   1158
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  7.34 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 22.53 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.26), residues: 1035
  helix:  1.65 (0.30), residues: 311
  sheet: -0.62 (0.35), residues: 218
  loop : -1.41 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 742 
 TYR   0.024   0.001   TYR A 371 
 PHE   0.019   0.002   PHE A 900 
 TRP   0.043   0.002   TRP A 258 
 HIS   0.005   0.001   HIS A 475 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8779)
  covalent geometry    : angle       0.62475 (11849)
  SS BOND              : bond        0.00067 (    1)
  SS BOND              : angle       1.11966 (    2)
  hydrogen bonds       : bond        0.03467 (  298)
  hydrogen bonds       : angle       4.58862 (  816)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 185
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.7567 (tp40) cc_final: 0.7236 (tm-30)
REVERT: A   20 ARG cc_start: 0.7901 (tpp-160) cc_final: 0.7184 (tmm-80)
REVERT: A   64 PHE cc_start: 0.7708 (p90) cc_final: 0.7419 (p90)
REVERT: A   69 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7309 (mm-30)
REVERT: A  135 ASN cc_start: 0.8433 (t0) cc_final: 0.7515 (p0)
REVERT: A  190 ILE cc_start: 0.8343 (mp) cc_final: 0.8073 (mp)
REVERT: A  210 MET cc_start: 0.8005 (mmm) cc_final: 0.7433 (mmm)
REVERT: A  355 CYS cc_start: 0.6942 (t) cc_final: 0.6523 (m)
REVERT: A  359 ASP cc_start: 0.6106 (m-30) cc_final: 0.5773 (m-30)
REVERT: A  379 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7538 (mmtt)
REVERT: A  548 GLN cc_start: 0.9085 (pt0) cc_final: 0.8575 (pm20)
REVERT: A  658 ASP cc_start: 0.8932 (m-30) cc_final: 0.8439 (m-30)
REVERT: A  700 ARG cc_start: 0.9140 (ttp80) cc_final: 0.8560 (ttp80)
REVERT: A  701 HIS cc_start: 0.7753 (OUTLIER) cc_final: 0.7517 (m-70)
REVERT: A  897 PHE cc_start: 0.8674 (t80) cc_final: 0.7860 (t80)
REVERT: A  946 ASN cc_start: 0.7737 (t0) cc_final: 0.7234 (t0)
REVERT: A  978 ASN cc_start: 0.8044 (m-40) cc_final: 0.7514 (t0)
REVERT: A 1009 MET cc_start: 0.6985 (mtt) cc_final: 0.6619 (mtt)
REVERT: A 1152 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8306 (p)
  outliers start: 42
  outliers final: 29
  residues processed: 209
  average time/residue: 0.0627
  time to fit residues: 18.9154
Evaluate side-chains
  210 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 178
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  365 ASP
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  701 HIS
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  722 LYS
Chi-restraints excluded: chain A residue  728 LYS
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1123 GLU
Chi-restraints excluded: chain A residue 1135 VAL
Chi-restraints excluded: chain A residue 1142 PHE
Chi-restraints excluded: chain A residue 1152 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 51 optimal weight:    9.9990
   chunk 24 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 96 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 527 HIS
A1025 HIS
** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.138729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.105321 restraints weight = 13757.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.109528 restraints weight = 6020.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.112194 restraints weight = 3532.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.113940 restraints weight = 2507.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.115217 restraints weight = 1994.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.5487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8780  Z= 0.174
  Angle     :  0.649   9.545  11851  Z= 0.336
  Chirality :  0.042   0.247   1273
  Planarity :  0.004   0.051   1521
  Dihedral  :  5.958  55.888   1157
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  8.21 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 23.05 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.51 (0.26), residues: 1035
  helix:  1.66 (0.30), residues: 311
  sheet: -0.65 (0.35), residues: 222
  loop : -1.51 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  41 
 TYR   0.025   0.002   TYR A 371 
 PHE   0.021   0.002   PHE A 272 
 TRP   0.028   0.002   TRP A 258 
 HIS   0.009   0.001   HIS A 475 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 8779)
  covalent geometry    : angle       0.64856 (11849)
  SS BOND              : bond        0.00167 (    1)
  SS BOND              : angle       0.83108 (    2)
  hydrogen bonds       : bond        0.03738 (  298)
  hydrogen bonds       : angle       4.66254 (  816)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 173
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.7626 (tp40) cc_final: 0.7374 (tm-30)
REVERT: A   20 ARG cc_start: 0.7953 (tpp-160) cc_final: 0.7248 (tmm-80)
REVERT: A   64 PHE cc_start: 0.7817 (p90) cc_final: 0.7533 (p90)
REVERT: A   69 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7378 (mm-30)
REVERT: A  190 ILE cc_start: 0.8392 (mp) cc_final: 0.8113 (mp)
REVERT: A  200 GLU cc_start: 0.8061 (tp30) cc_final: 0.7817 (tp30)
REVERT: A  210 MET cc_start: 0.8061 (mmm) cc_final: 0.7379 (mmm)
REVERT: A  359 ASP cc_start: 0.6368 (m-30) cc_final: 0.6036 (m-30)
REVERT: A  361 TRP cc_start: 0.8223 (m100) cc_final: 0.7758 (m100)
REVERT: A  379 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7644 (mmtp)
REVERT: A  487 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8238 (mt)
REVERT: A  548 GLN cc_start: 0.9104 (pt0) cc_final: 0.8589 (pm20)
REVERT: A  658 ASP cc_start: 0.8948 (m-30) cc_final: 0.8475 (m-30)
REVERT: A  700 ARG cc_start: 0.9131 (ttp80) cc_final: 0.8872 (ttp80)
REVERT: A  978 ASN cc_start: 0.8092 (m-40) cc_final: 0.7544 (t0)
REVERT: A  985 VAL cc_start: 0.7415 (t) cc_final: 0.6404 (p)
REVERT: A 1009 MET cc_start: 0.7191 (mtt) cc_final: 0.6757 (mtt)
REVERT: A 1039 GLN cc_start: 0.8218 (mt0) cc_final: 0.7827 (mt0)
REVERT: A 1152 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8342 (p)
  outliers start: 36
  outliers final: 27
  residues processed: 190
  average time/residue: 0.0663
  time to fit residues: 17.7682
Evaluate side-chains
  192 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 162
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   44 GLN
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  365 ASP
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  901 GLN
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1060 LEU
Chi-restraints excluded: chain A residue 1123 GLU
Chi-restraints excluded: chain A residue 1135 VAL
Chi-restraints excluded: chain A residue 1142 PHE
Chi-restraints excluded: chain A residue 1152 THR
Chi-restraints excluded: chain A residue 1177 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 22 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   overall best weight:    1.0586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1025 HIS
** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.140554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.107248 restraints weight = 13724.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.111431 restraints weight = 5973.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.114220 restraints weight = 3508.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.116087 restraints weight = 2468.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.117166 restraints weight = 1945.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.5674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8780  Z= 0.150
  Angle     :  0.636   9.590  11851  Z= 0.330
  Chirality :  0.042   0.223   1273
  Planarity :  0.004   0.049   1521
  Dihedral  :  5.900  55.774   1157
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  8.21 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 23.68 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.26), residues: 1035
  helix:  1.66 (0.30), residues: 311
  sheet: -0.65 (0.34), residues: 227
  loop : -1.57 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 235 
 TYR   0.025   0.001   TYR A 371 
 PHE   0.035   0.002   PHE A 272 
 TRP   0.020   0.001   TRP A 258 
 HIS   0.005   0.001   HIS A 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8779)
  covalent geometry    : angle       0.63601 (11849)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       0.95682 (    2)
  hydrogen bonds       : bond        0.03617 (  298)
  hydrogen bonds       : angle       4.65138 (  816)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 170
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.7911 (tpp-160) cc_final: 0.7173 (tmm-80)
REVERT: A   64 PHE cc_start: 0.7736 (p90) cc_final: 0.7424 (p90)
REVERT: A  210 MET cc_start: 0.8030 (mmm) cc_final: 0.7407 (mmm)
REVERT: A  271 LYS cc_start: 0.8389 (tptm) cc_final: 0.8039 (tppt)
REVERT: A  359 ASP cc_start: 0.6170 (m-30) cc_final: 0.5853 (m-30)
REVERT: A  361 TRP cc_start: 0.8176 (m100) cc_final: 0.7692 (m100)
REVERT: A  487 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8181 (mt)
REVERT: A  548 GLN cc_start: 0.9121 (pt0) cc_final: 0.8621 (pm20)
REVERT: A  658 ASP cc_start: 0.8944 (m-30) cc_final: 0.8451 (m-30)
REVERT: A  700 ARG cc_start: 0.9111 (ttp80) cc_final: 0.8873 (ttp80)
REVERT: A  903 ILE cc_start: 0.8449 (mt) cc_final: 0.8215 (tt)
REVERT: A  978 ASN cc_start: 0.8047 (m-40) cc_final: 0.7535 (t0)
REVERT: A  985 VAL cc_start: 0.7328 (t) cc_final: 0.6388 (p)
REVERT: A 1009 MET cc_start: 0.7143 (mtt) cc_final: 0.6774 (mtt)
REVERT: A 1039 GLN cc_start: 0.8148 (mt0) cc_final: 0.7755 (mt0)
REVERT: A 1141 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8033 (mpp)
REVERT: A 1152 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8331 (p)
  outliers start: 34
  outliers final: 27
  residues processed: 187
  average time/residue: 0.0582
  time to fit residues: 15.4613
Evaluate side-chains
  191 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 161
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   44 GLN
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  365 ASP
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  901 GLN
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1123 GLU
Chi-restraints excluded: chain A residue 1135 VAL
Chi-restraints excluded: chain A residue 1141 MET
Chi-restraints excluded: chain A residue 1142 PHE
Chi-restraints excluded: chain A residue 1152 THR
Chi-restraints excluded: chain A residue 1177 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 85 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 54 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 84 optimal weight:    0.0770
   chunk 53 optimal weight:    7.9990
   chunk 63 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.6738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1025 HIS
** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.141697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.108600 restraints weight = 13714.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.112905 restraints weight = 5932.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.115628 restraints weight = 3445.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.117539 restraints weight = 2428.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.118914 restraints weight = 1902.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.5866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8780  Z= 0.129
  Angle     :  0.628   9.357  11851  Z= 0.325
  Chirality :  0.041   0.204   1273
  Planarity :  0.004   0.050   1521
  Dihedral  :  5.761  51.309   1157
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  7.92 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 23.58 %
    Favored  : 72.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.26), residues: 1035
  helix:  1.72 (0.30), residues: 312
  sheet: -0.62 (0.34), residues: 235
  loop : -1.61 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 235 
 TYR   0.026   0.001   TYR A 371 
 PHE   0.028   0.002   PHE A 272 
 TRP   0.017   0.001   TRP A 258 
 HIS   0.005   0.001   HIS A 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8779)
  covalent geometry    : angle       0.62803 (11849)
  SS BOND              : bond        0.00005 (    1)
  SS BOND              : angle       0.93366 (    2)
  hydrogen bonds       : bond        0.03444 (  298)
  hydrogen bonds       : angle       4.56990 (  816)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 172
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.7898 (tpp-160) cc_final: 0.7157 (tmm-80)
REVERT: A   64 PHE cc_start: 0.7662 (p90) cc_final: 0.7350 (p90)
REVERT: A  210 MET cc_start: 0.8020 (mmm) cc_final: 0.7428 (mmm)
REVERT: A  359 ASP cc_start: 0.6038 (m-30) cc_final: 0.5807 (m-30)
REVERT: A  407 GLU cc_start: 0.6869 (tt0) cc_final: 0.6622 (tt0)
REVERT: A  419 LYS cc_start: 0.8543 (ttmm) cc_final: 0.8208 (ttpt)
REVERT: A  487 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8187 (mt)
REVERT: A  548 GLN cc_start: 0.9123 (pt0) cc_final: 0.8624 (pm20)
REVERT: A  557 LYS cc_start: 0.6151 (mmtm) cc_final: 0.5089 (ptpt)
REVERT: A  658 ASP cc_start: 0.8916 (m-30) cc_final: 0.8416 (m-30)
REVERT: A  700 ARG cc_start: 0.9078 (ttp80) cc_final: 0.8851 (ttp80)
REVERT: A  903 ILE cc_start: 0.8487 (mt) cc_final: 0.8273 (tt)
REVERT: A  978 ASN cc_start: 0.8067 (m-40) cc_final: 0.7588 (t0)
REVERT: A  985 VAL cc_start: 0.7267 (t) cc_final: 0.6956 (t)
REVERT: A 1039 GLN cc_start: 0.8092 (mt0) cc_final: 0.7762 (mt0)
REVERT: A 1152 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8315 (p)
  outliers start: 34
  outliers final: 28
  residues processed: 188
  average time/residue: 0.0668
  time to fit residues: 17.9155
Evaluate side-chains
  194 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 164
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   44 GLN
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  365 ASP
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  728 LYS
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  901 GLN
Chi-restraints excluded: chain A residue 1005 CYS
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1135 VAL
Chi-restraints excluded: chain A residue 1142 PHE
Chi-restraints excluded: chain A residue 1152 THR
Chi-restraints excluded: chain A residue 1177 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 103 optimal weight:    0.8980
   chunk 48 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 91 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1025 HIS
** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.141765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.108940 restraints weight = 13652.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.113168 restraints weight = 6061.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.115837 restraints weight = 3568.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.117633 restraints weight = 2515.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.118692 restraints weight = 1997.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.5968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8780  Z= 0.135
  Angle     :  0.634   9.173  11851  Z= 0.326
  Chirality :  0.041   0.198   1273
  Planarity :  0.004   0.049   1521
  Dihedral  :  5.637  49.573   1155
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  7.92 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 24.00 %
    Favored  : 72.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.49 (0.26), residues: 1035
  helix:  1.69 (0.30), residues: 312
  sheet: -0.60 (0.35), residues: 226
  loop : -1.54 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 235 
 TYR   0.029   0.001   TYR A 371 
 PHE   0.021   0.002   PHE A 272 
 TRP   0.016   0.001   TRP A 145 
 HIS   0.004   0.001   HIS A 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8779)
  covalent geometry    : angle       0.63346 (11849)
  SS BOND              : bond        0.00004 (    1)
  SS BOND              : angle       1.02002 (    2)
  hydrogen bonds       : bond        0.03446 (  298)
  hydrogen bonds       : angle       4.57789 (  816)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1517.12 seconds
wall clock time: 26 minutes 41.90 seconds (1601.90 seconds total)